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Biodiversity Catalogue
Niall BeardDr Aleksandra Nenadic
Prof Carole GobleeScience Lab, University of Manchester
Overview• Motivation: Web services discovery problem• Structure of Service Metadata• Ontological Classification• Features• Site Statistics• Remarks
• http://biodiversitycatalogue.org
Web Services DiscoveryHow can I advertise my Web services? What information do
people need about them?
What can this Web service do? How do I
use it? How do I know the Web service will still
be working tomorrow?
How can I find the right Web service?
WebService Provider
Scientist
What is BiodiversityCatalogue?
Register a WS
Find a WS
Use a WS
Invoke a WS/Get results
Scientist
Web Service
Service Provider
Faceted Browsing
11/06/2014 5
Tags
Available filters (below)
Applied filters (top)Result/filtered services
Subscribe to these filtersFurther searchingFilters
• Web service MONITORING– Services change and
get outdated– Long term reliability– Testing on a daily basis
Monitoring
11/06/2014 pro-iBiosphere Final Event, Brussels 6
Taverna WorkflowsInclude in Workflow
Taverna Workflows
Workflows in myExperiment.
org• myExperiment is
a Workflow registry
• Can integrate workflows within workflows using Taverna
Other Features
• Data Search – Search using your data to find services with corresponding input output types
• Script Testing (Defunct) – Write tests to check the operational functionality of the web service
Structure of Service Metadata• Profile• Documentation URL• Description• License• Cost• Contact Info• Usage Conditions• How to cite• Publications about service• Example workflows• Maturity
Structure of Service Metadata• Technical•Description of endpoints/operations•Example endpoints•Documentation URLs• Input Parameters
– Description– Default Value– Constrained Values– Example Data– Required or Optional
• Output Representations– Content Type (e.g. text/csv)– Example data– Data formats– Data Schemas– Tags
Topic Ontology• Controlled
Vocabulary used to classify Web services
• Privately constructed CV
• Mapped to EDAM to make outwardly interoperable
Bio.tools Integration• BioCatalogue exports its tools to the bio.tools registry
• Bio.tools uses the EDAM ontology to annotate.• Topic• Data• Format• Operation
• Unfortunately no such detail ontology tagging beyond topics
Bio.tools Tool Description
Data or Format Operation Data or Format
NB: Classifications are not disjoint
Remarks• Annotations work well for assisting
construction of workflows– Structured enough to help humans read– Free text annotations mean no service type or
domain knowledge needed. • Semantic annotations would work better– Automated workflow construction would be the
holy grail– Curation costs prohibitive
Example Data Services
• Ecological Niche Modelling with OpenModeller• https://www.biodiversitycatalogue.org/serv
ices/1